HsaINT0144195 @ hg19
Intron Retention
Gene
ENSG00000143171 | RXRG
Description
retinoid X receptor, gamma [Source:HGNC Symbol;Acc:10479]
Coordinates
chr1:165376049-165377555:-
Coord C1 exon
chr1:165377464-165377555
Coord A exon
chr1:165376155-165377463
Coord C2 exon
chr1:165376049-165376154
Length
1309 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACC
5' ss Score
8.66
3' ss Seq
AACTCAGTCATGTCTTTTAGATG
3' ss Score
6.07
Exon sequences
Seq C1 exon
AGTCCTAACTGAGCTGGTTTCCAAAATGAAAGACATGCAGATGGACAAGTCGGAACTGGGATGCCTGCGAGCCATTGTACTCTTTAACCCAG
Seq A exon
GTAACCGCCCTTCAACCCCAGGGGATGTGTGTGTTCAGCCCTCTTCCACGGTCAACCTCCAGTGCTCCCATGTTATTGGTCCTCCATCTCAGCTGAGACACAGATGGCAGAGCCAGGAATCCAGGAGAGCTCACAGTGTCAGCTAGAGCCATTTTGGAAAATGTTTTGAATGAGTGTGGCAGGCGCGTGTCTGGGGCAAGTGGGGAAGATGAAAGATGACGGTGGCCCAGGGTGGCAGTGAAGGGGGTGGTAAAAAGCGATCACATTCTGGATATATTTCTAGATAAAGCCACTGTGATTTGCTGATGGATTGAATATAGAATGAGAAAGAAAGAAAGGAGTTATAGATGACTCTCTGGGTTTTTTTTTTTTTAAGTTTTGTTTTCCTGAACAATGGGAAAAATGAAGTTCTTATTCACCGAGATGGGGAAAACTCCATGAGGAGCAAGTTCTGACAGCGGGTGGGTAGGAATCGGGATCTTGTCTTTGGACATTAAAATAGGAAATGGGTAGTAGATATCCAAGAGTGGCTGCCCAGGAAGCAACTGCTCATATGAGTCTGGACTTCATGGGAGAAGCCATGTGCATCTGAGAGCTGTCAGCCTCTGCCTGTGTAAGGCTGTGACACTGGGGTGAGATCATCTGGGGAGATAGAGCAGAGAAGATGGCTGGGGACTGAGCCCTGGGGCATGCCAACATTTAGAGGTCAGGTAAAAAAGGGAGAGCCAGCAGAGGAACCTGAGAAGGGGCAGGCAGTGAGATAGGGACAGAATCAGAAGGGTGGTGTCCTGGAGGCTCGAGGGAAAATAGTCTTTCAAGAAGGAGGCGATCAGCTCCAGCAAACCCTGCTGTGGTCAAGAAAGATGAACCTTCAGAATTATGTAGTCATTCATGCAGAGGCTTTATCTCCAGAATTAGGCAGTTAGTTCATCAATGCAGGACATGTGCCAATTCAGCTTTCGTGCCCCATCTTATGACTCAGTCCATGCTCAGCACATAATAGGCACTCGGTAAATGTGTGCAGGTAATATTTCGAGAATGGTCCGGATAAAATTAAGCTCTCCTCCTTAGAGTCAGTGGTGGGTACATTTGCCTATTCATGGAGTTTAAAATCTTTGCCCCAAGAGTTTGTTGGGTAAATTGGGCACAGAAAGAAGAGCAAGGGGGCATGAATGACCAGCTTTGTTTATTTCACACTTGTCCCCATCCAGGGTGTCTCTAGTAACTCTACAGAGAGTGGCCAGAGAGAATGGGGACAGCCTCTGCTGGAGGGTGTGTAATCAAAGGCTAACTCAGTCATGTCTTTTAG
Seq C2 exon
ATGCCAAGGGCCTGTCCAACCCCTCTGAGGTGGAGACTCTGCGAGAGAAGGTTTATGCCACCCTTGAGGCCTACACCAAGCAGAAGTATCCGGAACAGCCAGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143171-RXRG:NM_006917:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(16.0=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(18.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCCTAACTGAGCTGGTTTCCA
R:
CTGCCTGGCTGTTCCGGATA
Band lengths:
198-1507
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)